Detection of Bacillus spores is of considerable importance to the food industry since they can survive standard processing procedures and sanitation treatments. Surface enhanced Raman spectroscopy (SERS) coupled with gold SERS-active substrates was used to detect and discriminate among five Bacillus spores (B. cereus ATCC 13061, B. cereus ATCC 10876, B. cereus sp., B. subtilis sp., and B. stearothermophilus sp.). Tremendously enhanced Raman signals of Bacillus spores deposited onto the gold substrates were detected, allowing the limit of detection (LOD) of SERS to reach the level of a single spore. Distinct spectral differences were observed between different Bacillus spores. Hierarchical cluster analysis (HCA) and principle component analysis (PCA) show clear data segregations at the species level between five Bacillus spores. Principle component (PC) values indicate that the Raman shift range between 900 and 1200 cm -1 contributed significantly to the total data variance in the PCA results. In particular, a prominent band of dipicolinic acid (DPA) was observed at 998 cm -1 and served as a biomarker for bacterial spores. This study demonstrates that SERS coupled with gold nanosubstrates is able to detect and discriminate single Bacillus spores non-destructively and with minimum sample preparation. SERS method is a promising tool for rapid, ultra-sensitive, and selective detection of bacterial spores, potentially in foods and other complex biological matrices.